Protein Dynamic Processes Acquisition Based On Cryo-EM

Proteins in living organisms often exist in multiple conformations,and in-depth study of the multiple conformations of proteins can deepen understanding of the composition and function of life systems and promote the development of life science.Cryo-electron microscope(cryo-EM)technology has become one of the most important methods in the study of protein dynamic processes due to its ability to image samples under physiological conditions without the need for protein crystallization.However,traditional cryo-EM software has bottlenecks in processing protein dynamic processes,such as large amounts of data and difficulties in data analysis,which limit in-depth research on protein dynamic processes.Aiming at the problem that the algorithms currently used in cryo-EM reconstruction software are prone to mistakenly reconstruct small changes in proteins into high-resolution structures,resulting in the loss of important multiconformational structural information,a novel algorithm combining VGG16 network extraction depth features with K-means has been developed.The VGG16 convolutional neural network is used to extract deep features of protein change sites,and K-means is used to cluster particle images based on features to achieve the classification of small changes in proteins.The effectiveness of the algorithm has been verified in multiple protein systems,providing a reference for subsequent researchers on research methods for capturing protein dynamic processes with cryo-EM.In this paper,aiming at the problem of ambiguity in the signal transduction process of cannabinoid drugs,the cannabinoid receptor 1(CB1)-G protein was reconstructed based on the results of our algorithm and successfully obtained two consecutive intermediate conformations.Through analysis and verification,it is determined that Gα_idraw near the non-transmembrane region of CB1 and deep into GβAnd Gγ.The dynamic process of cannabinoid drug signal transduction provides a molecular mechanism reference for the subsequent design of targeted cannabinoid drugs.In this paper,aiming at the ambiguity of the degradation process of endoplasmic reticulum proteins,the ubiquitin protein ligase Hrd1 and membrane protein Hrd3complex was reconstructed based on the results of our algorithm and successfully captured three consecutive intermediate conformations.Through analysis and verification,the changes in the angle and spatial distance of Hrd1-Hrd3 were determined,thereby inferring the reverse transport of substrates during protein degradation by the endoplasmic reticulum,providing important theoretical support for the research of new targets for related diseases.To sum up,this article has established a new cryo-EM two-dimensional image clustering algorithm.By applying this algorithm to two important physiological protein systems,it has successfully achieved the capture of multiconformation structures during the dynamic process of proteins,breaking through the difficulties existing in cryo-EM technology in the study of multiconformation of proteins.